The higher sequence complexity of longer DNA molecules makes complete denaturation and re-annealing steps more difficult to achieve. As such, many state-of-the art analytical methods for the analysis of DNA (such as those that use microarrays, PCR amplification, or next generation sequencing) intentionally fragment DNA targets. However, once the original template DNA is fragmented, accurate assembly of the sequence for highly repetitive regions can be difficult, and long-range haplotype information may be lost. This disclosure provides a robust method to label, select, and/or manipulate longer DNA molecules.